Hi Elaine, There has been a recent message on the pdb2pqr/apbs bb about transferring the programs to a new site: http://apbs-rest-test.westus2.cloudapp.azure.com/ Would it be possible to access APBS via Chimera in the new location? Below please find pasted the message from Nathan Baker about the site change: ------------------------ Hello – I’m sorry about the problems you are experiencing. Can you please let us know if you are using http://apbs-rest-test.westus2.cloudapp.azure.com/ or http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ when you encounter this problem? Thank you, -- Nathan Baker Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab Department of Applied Mathematics — University of Washington +1-509-375-3997 — https://www.linkedin.com/in/nathanandrewbaker/ --------------------------------- Stay safe! Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of chimera-users-request@cgl.ucsf.edu <chimera-users-request@cgl.ucsf.edu> Sent: Friday, April 24, 2020 6:03 AM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 204, Issue 25 Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Autodock Vina, APBS, PDB2PQR web services will be removed (Elaine Meng) 2. Re: Autodock Vina, APBS, PDB2PQR web services will be removed (Gregory Babbitt) 3. Re: Autodock Vina, APBS, PDB2PQR web services will be removed (Elaine Meng) 4. Re: Imagine processing from gromacs (benjamintam) 5. Session opening issue (Zheng, Fengwei) ---------------------------------------------------------------------- Message: 1 Date: Thu, 23 Apr 2020 15:20:14 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> To: "chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Message-ID: <D0F537B2-0035-4D11-99A5-37D783428E2B@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Dear Chimera users, The Autodock Vina, APBS, and PDB2PQR tools in Chimera rely on web services provided by another lab, the National Biomedical Computation Resource. However, these web services are scheduled to be retired on April 30, 2020. When that happens, the Autodock Vina, APBS, and PDB2PQR tools in Chimera will no longer work, except for the (very few) people who use the tools to run locally installed copies of the program instead of the web services. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco ------------------------------ Message: 2 Date: Thu, 23 Apr 2020 22:30:14 +0000 From: Gregory Babbitt <gabsbi@rit.edu> To: "chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Message-ID: <1587681014069.66026@rit.edu> Content-Type: text/plain; charset="iso-8859-1" Thanks Elaine I am also curious about the future of the Modeller tool to refine loops via homology. will that also phase out? Dr. Gregory A Babbitt Associate Professor T.H. Gosnell School of Life Sciences Rochester Institute of Technology Rochester NY USA software website: http://people.rit.edu/gabsbi YouTube channel https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw ________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 23, 2020 6:20 PM To: chimera-users@cgl.ucsf.edu List Subject: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Dear Chimera users, The Autodock Vina, APBS, and PDB2PQR tools in Chimera rely on web services provided by another lab, the National Biomedical Computation Resource. However, these web services are scheduled to be retired on April 30, 2020. When that happens, the Autodock Vina, APBS, and PDB2PQR tools in Chimera will no longer work, except for the (very few) people who use the tools to run locally installed copies of the program instead of the web services. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 3 Date: Thu, 23 Apr 2020 15:39:07 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> To: Gregory Babbitt <gabsbi@rit.edu> Cc: "chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Autodock Vina, APBS, PDB2PQR web services will be removed Message-ID: <3E51C8AE-0F6C-4333-B665-D361CF8AC05D@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi Gregory, The other web services used by Chimera (Modeller, Blast Protein, Clustal Omega, MUSCLE, and others) won't be affected at this time because they're provided by our lab (RBVI), not the NBCR. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 23, 2020, at 3:30 PM, Gregory Babbitt <gabsbi@rit.edu> wrote:
Thanks Elaine
I am also curious about the future of the Modeller tool to refine loops via homology.
will that also phase out?
Dr. Gregory A Babbitt Associate Professor T.H. Gosnell School of Life Sciences Rochester Institute of Technology Rochester NY USA software website: http://people.rit.edu/gabsbi YouTube channel https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw
------------------------------ Message: 4 Date: Fri, 24 Apr 2020 02:36:10 +0000 From: benjamintam <benjamintam@um.edu.mo> To: chimera-users <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Imagine processing from gromacs Message-ID: <a758179c585148ca91c07ceefbbc1134@UMMBX3.pclan.umac.mo> Content-Type: text/plain; charset="us-ascii" Hi Eric, Thank you very much for your help. Although I am not sure whether is the university or the mailing list blocked the code content. Nevertheless, I appreciate your help. Best regards, Ben Ph.D, M.Eng, FHEA From: Eric Pettersen<mailto:pett@cgl.ucsf.edu> Sent: 24 April 2020 02:51 To: benjamintam<mailto:benjamintam@um.edu.mo> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Imagine processing from gromacs Hi Ben, Typically, one "wraps" a PBC trajectory to produce a new trajectory where molecules stay whole on one side of the box or the other. For Gromacs, the tool for that is trjconv, perhaps with the "-pbc whole" flags. See this page: gmx trjconv - GROMACS 2018 documentation<https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2furldefense.proofpoint.com%2fv2%2furl%3fu%3dhttp%2d3A%5f%5fmanual.gromacs.org%5fdocumentation%5f2018%5fonlinehelp%5fgmx%2d2Dtrjconv.html%26d%3dDwMFaQ%26c%3dKXXihdR8fRNGFkKiMQzstu%2d8MbOxd1NuZkcSBymGmgo%26r%3dEElAJhvpEXZIOG4aO3Q%5f1Fg1wh%2diIcDTLJ2t8QVMlxU%26m%3dpJfYo02dBWyMImWhNt9SQhEshAF42kEnCABBWjH3NjM%26s%3dVfw1MLZfC1pHcWEsIFazzl3tZ%2d0l%2dfHmOMBi6IeaOBs%26e%3d&umid=1193A768-A400-A205-949C-BD11EB526413&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-17b8b3991cfc711054f4afcfdd51feb0f255c2ed>. If wrapping a trajectory is problematic for some reason, you could define a per-frame Python script to hide long bonds. I have attached such a script. To use it, in the MD Movie GUI choose the Per-Frame?Define script... menu entry, and in the resulting dialog change the script type to "Python" and use the "Insert text file" button near the button to insert the attached Python file. Then click OK. Long bonds should disappear and you can play your trajectory and bonds will be hidden and shown appropriately. --Eric Eric Pettersen UCSF Computer Graphics Lab